Crystal structure of 1,2,3,5-di-O-methyl­ene-α-d-xylo­furan­ose

Abstract

The title compound, C₇H₁₀O₅, was synthesized by reaction of d-xylose with paraformaldehyde. In the crystal, the central part of the mol­ecule consists of a five-membered C₄O ring with an envelope conformation, with the methine C atom adjacent to the O atom being the flap. The protected O atoms of both cyclic acetal groups are oriented so that the four chiral C atoms of the furan­ose part show an R configuration. C—H⋯O hydrogen bonds are present between adjacent mol­ecules, generating a three-dimensional network.

Related literature  

For the synthesis of 1,2,3,5-di-O-methyl­ene-α-d-xylose, see: Schmidt & Nieswandt (1949 ▸). For the synthesis and characterization of chiral 1,3-di­hydro­benzo[c]furan derivatives and their inter­mediates, see: Ewing et al. (2000 ▸).

Experimental  

Crystal data  

• C₇H₁₀O₅

• M _r = 174.15

• Orthorhombic

• a = 8.5509 (11) Å

• b = 8.6327 (11) Å

• c = 20.057 (3) Å

• V = 1480.6 (3) ų

• Z = 8

• Mo Kα radiation

• μ = 0.14 mm⁻¹

• T = 100 K

• 0.53 × 0.16 × 0.13 mm

Data collection  

• Bruker Kappa APEXII DUO diffractometer

• Absorption correction: multi-scan (Blessing, 1995 ▸) T _min = 0.707, T _max = 0.744

• 12973 measured reflections

• 1858 independent reflections

• 1667 reflections with I > 2σ(I)

• R _int = 0.048

Refinement  

• R[F ² > 2σ(F ²)] = 0.033

• wR(F ²) = 0.074

• S = 1.05

• 1858 reflections

• 110 parameters

• H-atom parameters constrained

• Δρ_max = 0.23 e Å⁻³

• Δρ_min = −0.20 e Å⁻³

Data collection: APEX2 (Bruker, 2008 ▸); cell refinement: SAINT (Bruker, 2008 ▸); data reduction: SAINT; program(s) used to solve structure: SHELXL97 (Sheldrick, 2008 ▸); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015 ▸); molecular graphics: DIAMOND (Brandenburg & Putz, 2005 ▸); software used to prepare material for publication: SHELXL2014.

Supplementary Material

CCDC reference: 1432701

Additional supporting information: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (, ).

DHA	DH	HA	D A	DHA
C1H1O3i	1.00	2.57	3.311(2)	131
C3H3BO1ii	0.99	2.54	3.458(2)	154
C4H4O4ii	1.00	2.46	3.406(2)	157
C5H5O2iii	1.00	2.41	3.385(2)	166
C7H7AO3iv	0.99	2.47	3.337(2)	147
C7H7BO5v	0.99	2.55	3.390(2)	142

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) ; (v) .

supplementary crystallographic information

S1. Comment

The synthesis of the protected sugar 1,2,3,5-di-O-methylene-α-D-xylofuranose has been well known for many years (Schmidt & Nieswandt, 1949), its crystal structure, however, remained undetermined. According to the structure analysis, which we would like to now report, the central part of the molecule consists of a five-membered C₄O ring, which is build by the carbon atoms C1, C4, C5 and C6 and show an envelope conformation (Fig. 1). The protected oxygen atoms of both cyclic acetal groups are oriented in a way so that the four chiral carbon atoms of the furanose part exhibit R-configuration. Compounds with similar structures have been obtained as intermediates by using 1,2-O-isopropylidene-α-D-xylofuranose as a protecting group to synthesize chiral 1,3-dihydrobenzo[c]furan derivatives (Ewing et al., 2000). In the crystal structure of the title compound, C—H···O hydrogen bonds between adjacent molecules are present [d(H···O) = 2.41–2.57 Å] (Table 1), generating a three-dimensional network (Fig. 2).

S2. Experimental

According to the literature (Schmidt & Nieswandt, 1949) a mixture of 7.5 g (50 mmol) D-xylose and 10.0 g (333 mmol) paraformaldehyde were heated to 373 K. After treating the mixture with 20 g (204 mmol) of concentrated phosphoric acid (85%) and subsequent cooling to room temperature, the mixture has been extracted five times with chloroform. The combined extracts were washed and dried over sodium sulfate. After evaporation of the solvent, the crude product was destilled under reduced presure using a 20 cm Vigreux column. The fraction at 363 K (0.1 mbar) contained 3.4 g (39%) of the title compound. Single crystals were obtained by recystallization from petroleum ether and colorless needles were formed suitable for X-ray analysis.

S3. Refinement

The title compound crystallizes in the non-centrosymmetric space group C222₁; however, in the absence of significant anomalous scattering effects, the Flack parameter is essentially meaningless. The H atoms in CH₂ and CH groups were placed in calculated positions with d(C—H) = 0.99 Å and d(C—H) = 1.00 Å and refined using a riding model, with U(H) set to 1.2 U_eq(C).

Figures

Fig. 1.

The structure of the title compound with displacement ellipsoids at the 50% probability level.

Fig. 2.

C—H···O hydrogen bonds (black dashed lines) between adjacent molecules in the crystal structure of the title compound (bc view).

Crystal data

C7H10O5	Dx = 1.563 Mg m−3
Mr = 174.15	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, C2221	Cell parameters from 1667 reflections
a = 8.5509 (11) Å	θ = 2.0–28.4°
b = 8.6327 (11) Å	µ = 0.14 mm−1
c = 20.057 (3) Å	T = 100 K
V = 1480.6 (3) Å3	Needle, colorless
Z = 8	0.53 × 0.16 × 0.13 mm
F(000) = 736

Data collection

Bruker Kappa APEXII DUO diffractometer	1858 independent reflections
Radiation source: fine-focus sealed tube	1667 reflections with I > 2σ(I)
Triumph monochromator	Rint = 0.048
φ scans, and ω scans	θmax = 28.4°, θmin = 2.0°
Absorption correction: multi-scan (Blessing, 1995)	h = −11→9
Tmin = 0.707, Tmax = 0.744	k = −11→11
12973 measured reflections	l = −26→26

Refinement

Refinement on F2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.033	H-atom parameters constrained
wR(F2) = 0.074	w = 1/[σ2(Fo2) + (0.0335P)2 + 0.5951P] where P = (Fo2 + 2Fc2)/3
S = 1.05	(Δ/σ)max < 0.001
1858 reflections	Δρmax = 0.23 e Å−3
110 parameters	Δρmin = −0.20 e Å−3
0 restraints	Extinction correction: SHELXL2014 (Sheldrick, 2015), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0061 (7)

Special details

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
O1	0.35776 (16)	0.73794 (16)	0.15438 (7)	0.0209 (3)
C1	0.2196 (2)	0.6569 (2)	0.17647 (10)	0.0183 (4)
H1	0.1430	0.7322	0.1957	0.022*
O2	0.23608 (16)	0.44818 (15)	0.09492 (7)	0.0200 (3)
C2	0.2642 (3)	0.5386 (3)	0.22854 (11)	0.0250 (5)
H2A	0.3352	0.5874	0.2614	0.030*
H2B	0.1689	0.5051	0.2526	0.030*
O3	0.33921 (17)	0.40599 (17)	0.20058 (7)	0.0224 (3)
C3	0.2474 (2)	0.3445 (2)	0.14901 (11)	0.0229 (4)
H3A	0.1413	0.3217	0.1662	0.027*
H3B	0.2941	0.2459	0.1335	0.027*
O4	0.28366 (16)	0.95180 (15)	0.08815 (8)	0.0229 (3)
C4	0.1535 (2)	0.5865 (2)	0.11288 (10)	0.0175 (4)
H4	0.0381	0.5689	0.1160	0.021*
O5	0.07534 (18)	0.81726 (16)	0.04937 (8)	0.0239 (4)
C5	0.1948 (2)	0.7043 (2)	0.05959 (10)	0.0185 (4)
H5	0.2246	0.6526	0.0168	0.022*
C6	0.3328 (2)	0.7957 (2)	0.08923 (10)	0.0186 (4)
H6	0.4287	0.7817	0.0613	0.022*
C7	0.1181 (2)	0.9509 (2)	0.08583 (11)	0.0213 (4)
H7A	0.0741	0.9467	0.1314	0.026*
H7B	0.0788	1.0454	0.0634	0.026*

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
O1	0.0202 (5)	0.0228 (5)	0.0195 (5)	−0.0066 (4)	−0.0026 (4)	0.0012 (4)
C1	0.0181 (7)	0.0197 (7)	0.0172 (7)	−0.0015 (6)	0.0024 (6)	−0.0010 (6)
O2	0.0258 (5)	0.0129 (5)	0.0213 (5)	0.0043 (4)	−0.0029 (4)	−0.0014 (4)
C2	0.0290 (8)	0.0283 (8)	0.0176 (7)	−0.0006 (7)	0.0028 (6)	0.0026 (6)
O3	0.0213 (5)	0.0241 (5)	0.0217 (5)	0.0026 (4)	−0.0023 (4)	0.0048 (5)
C3	0.0236 (8)	0.0181 (7)	0.0268 (8)	−0.0009 (6)	−0.0026 (6)	0.0042 (6)
O4	0.0200 (5)	0.0141 (5)	0.0347 (6)	−0.0002 (4)	0.0032 (5)	−0.0002 (5)
C4	0.0171 (6)	0.0139 (7)	0.0214 (7)	0.0012 (6)	−0.0024 (6)	−0.0014 (6)
O5	0.0275 (6)	0.0145 (5)	0.0297 (6)	0.0034 (4)	−0.0094 (5)	−0.0004 (5)
C5	0.0245 (7)	0.0149 (7)	0.0162 (7)	0.0041 (6)	−0.0023 (6)	−0.0026 (5)
C6	0.0190 (7)	0.0164 (7)	0.0205 (7)	0.0024 (5)	0.0046 (6)	0.0005 (6)
C7	0.0220 (7)	0.0153 (7)	0.0267 (8)	0.0002 (5)	0.0004 (6)	−0.0015 (7)

Geometric parameters (Å, º)

O1—C6	1.4147 (18)	C3—H3B	0.9900
O1—C1	1.4429 (17)	O4—C6	1.4119 (17)
C1—C2	1.509 (2)	O4—C7	1.4164 (18)
C1—C4	1.522 (2)	C4—C5	1.517 (2)
C1—H1	1.0000	C4—H4	1.0000
O2—C3	1.4099 (19)	O5—C7	1.4139 (18)
O2—C4	1.4333 (16)	O5—C5	1.4269 (17)
C2—O3	1.4272 (19)	C5—C6	1.539 (2)
C2—H2A	0.9900	C5—H5	1.0000
C2—H2B	0.9900	C6—H6	1.0000
O3—C3	1.4029 (18)	C7—H7A	0.9900
C3—H3A	0.9900	C7—H7B	0.9900
C6—O1—C1	109.33 (11)	C5—C4—C1	103.67 (11)
O1—C1—C2	109.50 (12)	O2—C4—H4	112.0
O1—C1—C4	103.92 (11)	C5—C4—H4	112.0
C2—C1—C4	113.81 (12)	C1—C4—H4	112.0
O1—C1—H1	109.8	C7—O5—C5	107.35 (11)
C2—C1—H1	109.8	O5—C5—C4	113.12 (13)
C4—C1—H1	109.8	O5—C5—C6	104.72 (10)
C3—O2—C4	111.67 (11)	C4—C5—C6	104.48 (12)
O3—C2—C1	112.60 (12)	O5—C5—H5	111.4
O3—C2—H2A	109.1	C4—C5—H5	111.4
C1—C2—H2A	109.1	C6—C5—H5	111.4
O3—C2—H2B	109.1	O4—C6—O1	113.30 (12)
C1—C2—H2B	109.1	O4—C6—C5	104.77 (11)
H2A—C2—H2B	107.8	O1—C6—C5	106.97 (11)
C3—O3—C2	109.98 (12)	O4—C6—H6	110.5
O3—C3—O2	111.43 (12)	O1—C6—H6	110.5
O3—C3—H3A	109.3	C5—C6—H6	110.5
O2—C3—H3A	109.3	O5—C7—O4	106.26 (12)
O3—C3—H3B	109.3	O5—C7—H7A	110.5
O2—C3—H3B	109.3	O4—C7—H7A	110.5
H3A—C3—H3B	108.0	O5—C7—H7B	110.5
C6—O4—C7	107.02 (11)	O4—C7—H7B	110.5
O2—C4—C5	105.46 (11)	H7A—C7—H7B	108.7
O2—C4—C1	111.11 (12)
C6—O1—C1—C2	154.82 (12)	O2—C4—C5—O5	151.81 (11)
C6—O1—C1—C4	32.88 (14)	C1—C4—C5—O5	−91.33 (14)
O1—C1—C2—O3	−74.81 (15)	O2—C4—C5—C6	−94.88 (12)
C4—C1—C2—O3	40.99 (18)	C1—C4—C5—C6	21.97 (14)
C1—C2—O3—C3	−52.63 (16)	C7—O4—C6—O1	−94.14 (14)
C2—O3—C3—O2	65.51 (15)	C7—O4—C6—C5	22.11 (15)
C4—O2—C3—O3	−65.43 (15)	C1—O1—C6—O4	96.17 (13)
C3—O2—C4—C5	162.32 (12)	C1—O1—C6—C5	−18.77 (14)
C3—O2—C4—C1	50.63 (15)	O5—C5—C6—O4	−4.41 (15)
O1—C1—C4—O2	79.61 (13)	C4—C5—C6—O4	−123.57 (12)
C2—C1—C4—O2	−39.42 (17)	O5—C5—C6—O1	116.12 (12)
O1—C1—C4—C5	−33.22 (14)	C4—C5—C6—O1	−3.04 (14)
C2—C1—C4—C5	−152.25 (13)	C5—O5—C7—O4	29.22 (16)
C7—O5—C5—C4	98.23 (14)	C6—O4—C7—O5	−32.32 (17)
C7—O5—C5—C6	−14.93 (15)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C1—H1···O3i	1.00	2.57	3.311 (2)	131
C3—H3B···O1ii	0.99	2.54	3.458 (2)	154
C4—H4···O4ii	1.00	2.46	3.406 (2)	157
C5—H5···O2iii	1.00	2.41	3.385 (2)	166
C7—H7A···O3iv	0.99	2.47	3.337 (2)	147
C7—H7B···O5v	0.99	2.55	3.390 (2)	142

Symmetry codes: (i) −x+1/2, y+1/2, −z+1/2; (ii) x−1/2, y−1/2, z; (iii) x, −y+1, −z; (iv) x−1/2, y+1/2, z; (v) x, −y+2, −z.